Pokémon Civil War
by TrainerBronze
Summary: The Pokedex Holders have to face another threat! However they won't be standing together… When a horrible accident breaks the trust between the Pokedex Holders, the Region Champions begin to declare War against other neighboring regions… It's a Civil War, question is, Whose Side Are You On?
1. A New Beginning

**Pokémon Civil War is an all-out Civil War between the Regions. This story will feature all Pokedex Holders except Trainers X and Y. The story takes place directly after the events of the Omega Ruby and Alpha Sapphire Manga Arc. And yes, there will be DEATH. Not going to say anything else! Please Rate, Review, and all that Jazz! Trainer Bronze signing off.**

 **The Pokedex Holders have to face another threat! However they won't be standing together… When a horrible accident breaks the trust between the Pokedex Holders, the Region Champions begin to declare War against other neighboring regions… It's a Civil War, question is, Whose Side Are You On?**

 **Pairings: Red & Yellow, Green & Blue, Gold & Crystal, Ruby & Sapphire, Diamond & Platinum, and Black & White. (Sorry Pearl)**

 **WARNING: THIS STORY WILL HAVE BLOOD, DEATH, AND SOME USE OF FOUL LANGUAGE.**

 **Chapter 1: A New Beginning**

 **XX Day of the XX Month**

"Why did you bring us all here today?"

"I believe we all have a lot in common…"

"What do you mean?"

"We've all been defeated by those pesky Pokedex Holders… We've all tried to have absolute power, and we've all failed…"

"…"

"I believe it is time for an alliance, so that we can bring down the Pokedex Holders for good…"

"But we can't beat them! They're too strong!"

"Yes, but what if they fought each other… What if their bond was to be broken, hm?"

"Then we wouldn't have to beat them! They would just beat themselves… But how will we do it?"

"We'll do it like so…"

 **March 3, Viridian City, Kanto**

"HAPPY BIRTHDAY YELLOW!" The Pokedex Holders yelled.

"You guys didn't have to…" Yellow said.

"But you're turning 20! We have to celebrate!" Blue gushed. The Dex Holders from all the regions,

Kanto, Johto, Hoenn, Sinnoh, and Unova had arrived to celebrate Yellow's birthday.

"I think everyone is here… Wait where is Gold?"

"He better not be doing what I think he is doing…" Crystal quickly rushed over to the kitchen. "GOLD! I TOLD YOU NO TOUCHING THE CAKE!"

"Aw come on Crys, it was just one piece…"

"WHY YOU- I'm GONNA GET YOU FOR RUINING YELLOW'S CAKE! WE HAD TO WAIT 2 HOURS FOR IT!" Crystal began to chase Gold out of the house while Gold screamed for help. Blue and Emerald kept on laughing while Green kept on mumbling about Blue being too annoying.

"Hey Red, are you ready for you know what with your girlfriend?" Blue asked while nudging him.

"Huh? Oh yeah… Um, I guess I am…"

"Good! Don't screw up then!" Blue skipped back over to Green who once again was mumbling something about Blue being pesky. Meanwhile Ruby and Sapphire were once again arguing about something. Platinum was talking with Emerald and seemed to be getting along quite well. Diamond was eating something while Pearl was talking with him. Black and White were both talking with Yellow as it was only the second time meeting her. Silver on the other hand was hanging around with Blue. Finally Crystal came back dragging Gold.

"I'm sorry Super Serious Gal…"

"DON'T EVEN THINK ABOUT IT! YOU HEAR ME!?" Gold squirmed in fear.

"Oh, now that Senior Crystal is back with Senior Gold, now we can start giving the gifts!" Platinum exclaimed.

Blue gave Yellow a new coloring set, a book from Green, a new dress from Ruby, a variety of berries from Sapphire, a collection of Pokeballs from Emerald, a pair of gloves from Silver, a sweater from Crystal, a Super Rod from Gold, a Castellia Cone Maker from Black & White, a necklace from Platinum, and finally a book about Sinnoh Pokémon from both Pearl & Diamond. The only person who was left was Red who was patiently waiting in the corner of the room.

"Red, isn't it time for your gift to your girlfriend?"

After learning about Yellow's feelings for him, Red had begun dating with Yellow for about half a year now. Red stopped leaning on the wall and seemed to be grabbing something in his pocket. Red walked over toward Yellow who was currently blushing very furiously. He took off his hat and grabbed both of Yellow's hands.

"He is going to do it…" Gold whispered to Crystal.

"Shut up, you're going to ruin the moment…"

Red then kneeled down on one knee and looked straight into Yellow's amber eyes. Yellow began to blush even more as she was quite confused.

"Yellow, we've known each other for many years and ever since we met in Viridian Forest I knew there was something different about you… Something special…"

Yellow's eyes began to water.

"Throughout these years I was completely oblivious that you actually liked me the entire time… You were and always so kind to me… I can't believe I never noticed that…"

A tear began to form in Yellow's eye.

"You're the kindest, sweetest, and most beautiful woman I have ever met... I may not be even good for you. In fact, you may be too good for me… Even now I had to muster all the courage I had, but Yellow Amarillo del Bosque Verde…"

The room went silent. Red pulled out a small box and opened it. In it was a Diamond Ring that glinted brightly. Yellow was now in tears.

"Will you marry me?"

"YES!" exclaimed Yellow as she then kissed Red on the lips and they both closed their eyes. The room went wild after that.

"HA SHE SAID YES! I KNEW IT! FINALLY! AFTER ALL THESE YEARS, MY LIFE IS NOW COMPLETE!" Gold yelled. All of the Pokedex Holders began to congratulate both Yellow and Red. All the boys surrounded Red while all the girls surrounded Yellow. All of the male Dex Holders were slapping Red on the back and high fiving him.

"See man, I knew you could pull it off!" Gold yelled as he wrapped his arm around his neck. Ruby then began to ramble on about getting the perfect suit for Red and how he needed to look perfect for the wedding. Both Silver and Green were actually smiling something that rarely ever happened. Emerald, Pearl, and Diamond were already asking about when the wedding would be. Red just kept on laughing.

On the girl's side, they all kept on screaming about the same thing. Wedding dresses, how did she feel and how they finally were getting married. Yellow was in tears saying it was the best birthday ever. Blue then skipped over to Green.

"See aren't they so cute together? Why can't you be like that huh? Why won't you propose to me?" Green sighed.

"You're so annoying…"

The males and females dispersed as Red and Yellow walked up to each other. Yellow was at lost for words. She wouldn't have to draw pictures of Red and daydream anymore. Because Red would be with her.

"You trust me right?"

Yellow nodded.

"I promise that we will live a happy life. No matter what happens. I promise."

Yellow nodded again. And they both embraced.

The next hours were paradise as all the Dex Holders began to celebrate with each other. Gold and Crystal were both getting drunk after drinking too many cans of beer. Ruby and Sapphire were yelling again about something while Emerald was trying to separate them. Blue was once again flirting with Green. Black and White though fairly new were both congratulating Yellow. Silver was talking with Red about future plans. And the Sinnoh trio Pearl, Diamond, and Platinum were laughing telling stories and jokes. Even as night began to settle they continued to party. Red held Yellow's hand. Yellow decided to allow the Dex Holders to stay for a few days before returning to their home regions. They all laughed, rejoiced, for it was a great day. However unknown to the Dex Holders an ominous figure stared at them through the window. The figure chuckled.

"Yes, celebrate. Rejoice while you still can, for the end times are coming. And when those times come, they will tear your friendship apart…" The figure then walked away into the deep night as the Dex Holders continued to party.

 **Thanks for reading! Wow that really escalated quickly and it's only the first chapter. And I have great news! I will consider putting in your own character into my story! I have a form just down below! Please note that I will not accept all submissions and not all characters will be featured immediately. Please understand!**

 **TRAINER FORM:**

 **Name:**

 **Nickname:**

 **Birthday:**

 **Gender:**

 **Age:**

 **Personality:**

 **Birthplace (City and Region):**

 **Pokémon Team:**

 **Occupation:**

 **OPTIONAL - Background Info (Origin, Tragedies, etc.):**

 **Thanks for reading. As always Rate, Review, Follow, or Fav! Hope you enjoy the start of this new adventure…**


	2. The Spark of a War

**So here is Chapter 2! I received some Trainer Form Applicants and I hope to be able to put them in my story. I have so far received 3 applicants so far, in which 2 of them will be featured in this chapter. I will try to include all characters, so if you don't see your character yet, I will include he or she soon! Thanks for the support, and here we go!**

 **Chapter 2: The Spark of a War**

 **XX Day of the XX Month**

"Everything is ready sir."

"Excellent. Remember, kill all that get in the way. But put the Target in priority."

"Yes sir."

 **SMASH!**

"Hey, what are you doing in my house?!"

"I'm sorry Professor that it had to be this way."

"Gold…?! What are you doing here?!"

"Kill him. Leave the body too."

"What are you- NO!"

 **SHINK.** Blood splattered throughout the room.

"Target Priority 1 has been eliminated. I repeat mission is success."

 **May 21, Littleroot Town, Hoenn**

Yuki walked toward the pathway to Littleroot Town. He was a bit too excited as he was going to meet Professor Birch. Professor Oak had sent Yuki to check on Birch to see why he was not responding to his messages. Yuki was not a Dex Holder but a well experienced trainer from the faraway region of Kalos.

"Wow, everything here is so different…" Yuki said under his breath. He finally arrived at the lab of Professor Birch. But the town seemed a bit quiet… Something wasn't right… Yuki gripped his Pokeball and slowly entered the lab. There he found a horrible sight. Yuki quickly grabbed his Pokegear and called Professor Oak.

"Professor, we might have a problem on our hands…"

 **May 22, Pallet Town, Kanto**

"Professor Birch is what?!" Ruby screamed.

"Dead. His body was just found yesterday by Yuki. I am expecting an autopsy report anytime… Sapphire, I am sorry. Professor Birch was a great man and friend." Oak stared at the Hoenn Dex Holder. Sapphire was in a corner holding on to her legs. After receiving the news, Sapphire went into deep shock.

"If only we had been in Hoenn, maybe we could have saved him…" Ruby mumbled. Ruby walked over to Sapphire and grabbed her shoulder. Sapphire normally would react in an abrupt manner, but instead she said nothing. Crystal stared at her 2 friends both now crying.

"Didn't Professor Birch always keep a surveillance camera in his lab?" Crystal asked. Professor Oak nodded.

"That's right. Police are currently looking at the footage now. What's interesting is that Birch's murderers did not seem to care that there was a camera. It is possible that whoever killed Birch did not notice the camera, but it still odd." Oak looked at Yuki. "Thank you for telling us about this immediately. I should perhaps introduce you. Crystal this is Yuki. He is from the Kalos region." Crystal shook hands with Yuki.

"A pleasure to meet you." Crystal said. Suddenly the door was slammed open, and all the Dex Holders began coming into the room.

"Why did you call us all Professor?" Red asked as he was holding Yellow's hand. All the Dex Holders, even Green had a curious face.

"I want you all to sit down right now please. I have unfortunate news." Ruby and Sapphire were still crying. Oak had a glum look on his face. "The reason why I have brought you all here today is because of an unfortunate death… Professor Birch of Hoenn… Is dead." The room erupted. All the Dex Holders began screaming, asking questions. Emerald walked over to Ruby and Sapphire to comfort them.

"Now, we don't know much as to how he died, but I believe I shall be receiving autopsies and surveillance footage soon."

Red's Pokegear began to ring. It was a call from Lance.

"Red, we are having an emergency League Champions meeting right now. I am requesting that you come immediately to the Kanto Pokémon League. It is involving the death of Professor Birch."

"Okay, I'll be there right away." Red responded. Red told the room about his sudden meeting and how he had to go. Yellow kissed Red on the cheek and told him to be safe.

"I'm coming with you Red." Oak said. "As Professor of Kanto I too must know what is going on. Yuki you're coming too." Red nodded and introduced himself to Yuki. Oak instructed all the Dex Holders to NOT leave Pallet Town until further instructions.

"It is best that you remain together for your own safety. No more shall die this week." Red sent out his Aero, Yuki sent out his Noivern, and Professor Oak sent out Fearow, and off they went. The other Pokedex Holders were silent, and the only noise that could be heard were the tears of Sapphire.

 **Kanto/Johto Pokémon League Champion Conference Room**

All the champions from all the regions arrived except for Kalos' champion. Red from Kanto, Lance who would be representing Johto, Steven from Hoenn, Cynthia from Sinnoh, and Alder from Unova. Professor Oak and Yuki stayed in the background. Steven started the meeting.

"All Champions are here except for the Kalos League Champion correct?" All the champions nodded. "As you all know Professor Birch of Hoenn was murdered…And here is the autopsy report." An autopsy report was handed out to everyone.

"According to the report Professor Birch died on May 20 at 11 PM. The cause of death was stab wound to the stomach, and continuous bleeding. It is possible that Professor Birch would have survived had his body was discovered sooner."

"And a Trainer by the name of Yuki discovered the body?" Cynthia asked. Steven nodded.

"In fact Trainer Yuki is here today along with Professor Oak of Kanto. Yuki would you care to explain what you saw?" Yuki nodded.

"My name is Yuki. I am a Trainer from the region of Kalos, but I am not a Pokedex Holder. Well it was just yesterday, May 21, at around 8 AM. Professor Oak had sent me to Littleroot Town, Hoenn to see why Professor Birch was not responding to his messages. When I arrived in town, it was quiet. Almost too quiet. I entered the laboratory and noticed papers everywhere. Then I saw what was blood, and the corpse of Professor Birch on the ground. I checked his pulse, and he was dead. I called Professor Oak and police soon arrived. That is all." All the Champions nodded.

"Now, in Professor's Birch lab is a video camera. When police inspected the camera, it was not tampered in any way. None of us including I have seen the footage…" Steven then held up a tape. "…Until now. The police just recently gave us the tape after reviewing it themselves. They say they have a clear suspect as to who the murderer may be." Steven placed the tape in a video player, and the lights went out.

The video footage was fast forwarded to 10:30 PM. It first showed Professor Birch talking with his wife.

 _"Are you sure you'll be okay by yourself dear?"_

 _"Yes it will be okay. You'll return in a week correct?"_

 _"Yes, stay safe. Sapphire should return in a few days."_

 _"Have a nice trip honey!"_

Steven paused the video footage.

"This was the last hour of Professor Birch. His wife was going out to Unova to visit a friend. At the time, their daughter Sapphire Birch was in Kanto." Steven clicked play. The footage showed the Professor continuing to work on his computer and looking at books. The footage time was now 10:55 PM.

 _SMASH!_

 _"Hey, what are you doing in my house?!"_

 _"I'm sorry Professor that it had to be this way."_

 _"Gold…?! What are you doing here?!"_

 _"Kill him. Leave the body too."_

 _"What are you- NO!"_

 _SHINK._

Steven stopped the footage for a minute.

"Here we see Professor Birch being murdered. And he mentions someone named 'Gold'. I believe he is a Pokedex Holder from Johto correct?" Lance stared at the table. Red remained silent. "Let us continue the footage."

 _The murderer waves away the other 2 men. Then turns right toward the camera revealing the face of the murderer. The face strongly resembled,_ _ **Trainer Gold of Johto**_ _._

Red, Lance, and Professor Oak were speechless. Gold was never capable of this. Or was he?

 _Killer walks out of the lab. Professor Birch seen crawling over to his computer typing something. The Professor stares directly at the camera._

 _"…Tell my wife and Sapphire… I love them."_

Steven stops the footage. "We've seen enough."

"What was written on the computer screen when police arrived?" Cynthia asked.

"It was a word. Or a name. It showed ' _Gold_.'" Steven Stone stared at Lance. "Care to explain why Trainer Gold of Johto murdered Professor Birch of Hoenn!?" Steven began to raise his voice. Lance slammed his hand on the table.

"Nonsense! Gold would never do this!" Red also nodded agreeing to Lance's statement. Steven then slammed his hand on the table.

"If Gold is not turned over to Hoenn Authorities, The Region of Hoenn will declare WAR on the Region of Johto." Lance gaped.

"One murder is not a reason to declare War! You don't want another Great Pokémon War do you!?"

"I will take any measures to avenge the Professor! Even if it means war! In fact, we have more reasons to declare war on Johto!" Steven Stone slammed a folder of papers onto the table. "In here are the faults we put on the Region of Johto! Do you remember the Battle Frontier incident? We are placing all damages on the fault of Johto."

Professor Oak did not say a word. "We also have a reason to believe that the Region of Johto stole items from Hoenn and smuggled them into your own region! The list goes on!" Lance was beginning to lose his patience.

"We shall not hand over Gold to Hoenn Authorities!"

"I shall call a vote. Who believes Gold should be handed over to Hoenn authorities?" Steven, Alder, and Cynthia raised their hands. The only 2 who did not was Red and Lance. Steven stared at Red of Kanto.

"Champion of Kanto, you agree with Lance?" Red gripped his hat a bit tighter.

"I've known Gold for many years, and I know he would never do this. And if he did he must have a good reason to do so." Steven laughed.

"You Red are the youngest of all the Champions. I thought you would know better. His reasons will not revive Professor Birch! The Council of the Region Champions has agreed to take Gold into Hoenn authorities. If Gold is not handed over to authorities, Hoenn shall declare War on the region of Johto. All communications will be blocked. All who join Johto shall receive the same fate. You have 1 week to respond. Dismissed." All the Region Champions trailed out the room. Steven stopped at Lance.

"Are you really going to not give up 1 life for the sake of millions? You are stubborn and stupid. Johto scum. And you Red. I expected much more." Steven Stone also walked out of the Conference Room. Lance clenched his fist and gritted his teeth. Red walked over to Lance.

"If Steven truly intends to declare war on Johto, Kanto shall stand with you. But I hope it doesn't come to do that." Lance nodded.

"Gold would never do this... Professor Oak please send notify the Dex Holders in town of this. Tell them every detail. Red, Yuki, return to Pallet Town. I have a decision to make." Red, Yuki, and Oak left the Kanto/Johto Pokémon League. Red stretched out his arms.

"Will it really be war Professor?" Red asked. Professor Oak closed his eyes.

"I hope it doesn't. You have heard of the Great Pokémon War correct?" Red nodded. "Then I hope not."

In the mountains an unseen trainer was in the shadows. It was a female Trainer with a Golbat. The unknown trainer grinned.

"So it will be war then. Excellent. Humanity needs a wakeup call. Maybe this will help." Red, Yuki, and Oak unaware of their eavesdropper walked away from the Pokémon League. The female trainer then flew off on her Golbat.

 **Hope you enjoyed this chapter! Shout-out to hugo17vm and Farla. Their characters were in this chapter. If your character was not mentioned yet, have no fear! I have not overlooked it or ignored it. They will be featured at one point or another. Your character can be in this story too! Check Chapter 1 to see the form application. You can PM me or comment in the review section if you want to submit your application. Thanks for reading and remember, Rate, Review, Follow, or Fav! Trainer Bronze signing out!**


End file.
